Mitochondria are an interesting target for drug delivery due to their role in energy production, reactive oxygen species production, and apoptosis. Drug delivery to the mitochondria is difficult due to the intricacies involved in crossing three diverse membranes: the plasma membrane, and the outer and inner mitochondrial membranes (OMM and IMM, respectively). Overcoming these challenges, a new class of synthetically designed peptides was recently discovered to penetrate the plasma membrane and target the mitochondria with high specificity, coined mitochondria-penetrating peptides (MPPs). By targeting the mitochondria directly, MPPs become a valuable vehicle for drug delivery. For instance, methotrexate is a powerful antibacterial agent, but accumulation in the cytosol of human cells renders it highly toxic and limits its therapeutic capabilities. By conjugating methotrexate to MPPs, the drug specifically targeted the mitochondria, decreasing the toxicity three orders of magnitude, while maintaining antibacterial activity. Recent studies have shown that membrane composition, specifically headgroup functionality, and transmembrane potential play important roles in membrane-peptide activity by controlling peptide binding and subsequent bilayer disruption or alteration.